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bioinformatics-centre / AsmVar

A software for discovery, genotyping and characterization of structural variants
http://bioinformatics-centre.github.io/AsmVar
MIT License
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Question on joint genotyping #2

Open ldorozco opened 6 years ago

ldorozco commented 6 years ago

I as wondering if AsmVar does "joint genotyping" of multiple samples, analogous to what GATK does for SNPs?

Does AsmVar do break-point resolution? For example, if I have a population samples with structural variants in the same region, can AsmVar use that information to try to figure out the boundaries of the structural variant?

Thank you,

Luz

ShujiaHuang commented 6 years ago

Hi @ldorozco , AsmVar does "joint genotyping" using Gaussian mixture model, different from the exact algorithm by GATK. AsmVar calls structural variant in break-point resolution since it calls variants from an de novo assembly. You must have the population samples assembled so as to figure out the boundaries of the structural variant.

ldorozco commented 6 years ago

Hi,

Thank you for your reply. I have one quick follow up. Does the genotyping option for AsmVar work only for variants called by AsmVar, or can it do joint genotyping given variants in a population sample?

Thank you for your time.

Luz

On Mon, Jul 24, 2017 at 2:16 AM, YellowTree notifications@github.com wrote:

Hi @ldorozco https://github.com/ldorozco , AsmVar does "joint genotyping" using Gaussian mixture model, different from the exact algorithm by GATK. AsmVar calls structural variant in break-point resolution since it calls variants from an de novo assembly. You must have the population samples assembled so as to figure out the boundaries of the structural variant.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/bioinformatics-centre/AsmVar/issues/2#issuecomment-317365462, or mute the thread https://github.com/notifications/unsubscribe-auth/AEEiyUp7JCb87j3pQEuaf_uXeI6r5Dsuks5sRGDVgaJpZM4Oeu3s .